[gmx-users] Protein-DNA simulation LINKS error
tyugashev at niboch.nsc.ru
Wed Jul 1 14:08:13 CEST 2015
Thanks for the advice, Justin and Mark.
After rerunning the simulation with guanine in the DNA I've found no
Now I'm looking for another possible sources for mistakes.
1.The input PDB file is formatted using amber conventions, i.e. DG5 and
DG3 for terminal guanosine residues, CYX for S--S linked cystine and so
on. Could it result in any erroneous interpretations by pdb2gmx?
2. I think I correctly created 8-oxoguanine entry in amber force field
files by copying and modifying existing one for normal guanine, but I
want to re-check myself just to be sure. Is there anything more in-depth
available than rather laconic instruction from the GROMACS site? I've
tried searching through the maillist, but looks like nothing similar
came up (It's a pity that no forum exist, looking for past answers would
be far simpler).
3. Could an accidental simultaneous execution of two or three jobs on
one workstation (scheduling script was set incorrectly once) cause LINKS
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